def run(self):
"""
02-01-06
"""
(conn, curs) = db_connect(self.hostname, self.dbname)
tax_id = get_tax_id_from_org(curs, self.organism)
mt_id2no = get_mt_id2no(curs, self.matrix_table)
prom_id2gene_id = self.get_prom_id2gene_id(curs, self.prom_seq_table, self.organism)
self.parse_input_fname(curs, self.input_fname, self.p_value_cut_off, prom_id2gene_id, mt_id2no, tax_id, self.output_table)
if self.commit:
curs.execute("end")
def run(self):
"""
02-01-06
"""
(conn, curs) = db_connect(self.hostname, self.dbname)
tax_id = get_tax_id_from_org(curs, self.organism)
mt_id2no = get_mt_id2no(curs, self.matrix_table)
prom_id2gene_id = self.get_prom_id2gene_id(curs, self.prom_seq_table,
self.organism)
self.parse_input_fname(curs, self.input_fname, self.p_value_cut_off,
prom_id2gene_id, mt_id2no, tax_id,
self.output_table)
if self.commit:
curs.execute("end")
def run(self):
"""
09-18-05
09-30-05
way of calling get_mt_id2no() changed
get gene_id_dict is a thread now, to speed up
"""
(conn, curs) = db_connect(self.hostname, self.dbname)
tax_id = org2tax_id(self.organism)
tax_id_set = Set([tax_id])
get_gene_id_dict_instance = get_gene_id_dict(self.acc_file, tax_id_set)
get_gene_id_dict_instance.start()
mt_id2no = get_mt_id2no(curs, self.matrix_table)
mt_no2matches = self.get_mt_no2matches(curs, self.input_table, self.prom_seq_table, self.top_number, self.organism, mt_id2no)
get_gene_id_dict_instance.join() #must wait it to finish before going on, need gene_id_dict
self.dump2output_table(curs, self.output_table, mt_no2matches, get_gene_id_dict_instance.gene_id_dict, tax_id)
if self.commit:
curs.execute("end")